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Identification and characterisation of G-quadruplex DNA-forming sequences in the Pseudomonas aeruginosa genome

Research output: Contribution to journalArticlepeer-review

Lindsay Evans, Anita Kotar, Martina Valentini, Alain Filloux, Shirin Jamshidi, Janez Plavec, Miraz Rahman, Ramon Vilar

Original languageEnglish
Number of pages18
JournalRSC Chemical Biology
DOIs
Published15 Nov 2022

Bibliographical note

Funding Information: This work was supported by the Engineering and Physical Research Council UK (EPSRC –grant to LE, KMR, AF and RV), the Biotechnology and Biological Sciences Research Council (BBSRC – grant BB/L007959/1 to AF), the Swiss National Science Foundation (grant P2LAP3-148450 to MV) and Slovenian Research Agency (grant P1-0242 to AK and JP). The authors acknowledge the CERIC-ERIC Consortium for the access to experimental facilities and financial support. Publisher Copyright: © 2022 RSC.

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Abstract

A number of Gram-negative bacteria such as Pseudomonas aeruginosa are becoming resistant to front-line antibiotics. Consequently, there is a pressing need to find alternative bio-molecular targets for the development of new drugs. Since non-canonical DNA structures such as guanine-quadruplexes (G4s) have been implicated in regulating transcription, we were interested in determining whether there are putative quadruplex-forming sequences (PQS) in the genome of Pseudomonas aeruginosa. Using bioinformatic tools, we screened 36 genes potentially relevant to drug resistance for the presence of PQS and 10 of these were selected for biophysical characterisation (i.e. circular dichroism and thermal difference UV/Vis spectroscopy). These studies showed that three of these G-rich sequences (linked to murE, ftsB and mexC genes) form stable guanine-quadruplexes which were studied by NMR spectroscopy; detailed analysis of one of the sequences (mexC) confirmed that it adopts a two-quartet antiparallel quadruplex structure in the presence of K+ ions. We also show by FRET melting assays that small molecules can stabilise these three new G4 DNA structures under physiological conditions. These initial results could be of future interest in the development of new antibiotics with alternative bio-molecular targets which in turn would help tackle antimicrobial resistance.

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